Archive BacDiveID:10.13145/bacdive11954.20230509.8.1

Strain identifier

BacDive ID: 11954

Type strain:

Species: Kurthia zopfii

Strain Designation: F 64/100, EF 64/100

Strain history: CIP <- 1988, NCIB <- 1966, T. Gibson <- E.M. Barns: strain EF 64/100

NCBI tax ID(s): 1650 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 8930

BacDive-ID: 11954

DSM-Number: 20580

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, human pathogen

description: Kurthia zopfii F 64/100 is an aerobe, mesophilic, Gram-positive human pathogen of the family Caryophanaceae.

NCBI tax id

NCBI tax id: 1650
Matching level: species

strain history

@ref	history
8930	<- NCTC <- NCIB <- T. Gibson <- E.M. Barnes, F 64/100
67770	R. M. Keddie K5.
124037	CIP <- 1988, NCIB <- 1966, T. Gibson <- E.M. Barns: strain EF 64/100

doi: 10.13145/bacdive11954.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Bacilli
order: Caryophanales
family: Caryophanaceae
genus: Kurthia
species: Kurthia zopfii
full scientific name: Kurthia zopfii (Kurth 1883) Trevisan 1885 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Bacterium zopfii

@ref: 8930

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Kurthia

species: Kurthia zopfii

full scientific name: Kurthia zopfii (Kurth 1883) Trevisan 1885

strain designation: F 64/100, EF 64/100

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
8930	CORYNEBACTERIUM AGAR (DSMZ Medium 53)	yes	https://mediadive.dsmz.de/medium/53	Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
41347	MEDIUM 3 - Columbia agar	yes		Columbia agar (39.000 g);distilled water (1000.000 ml)
124037	CIP Medium 3	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@ref	growth	type	temperature	range
8930	positive	growth	30	mesophilic
41347	positive	growth	30	mesophilic
54532	positive	growth	30-37	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 54532
oxygen tolerance: aerobe

murein

@ref: 8930
murein short key: A11.31
type: A4alpha L-Lys-D-Asp

fatty acid profile

fatty acids

@ref	fatty acid	percentage	ECL
54532	C14:0	3.2	14
54532	C15:0	1.6	15
54532	C16:0	5.6	16
54532	C18:0	2.5	18
54532	C13:0 ANTEISO	0.4	12.701
54532	C13:0 iso	0.9	12.612
54532	C14:0 ISO	17	13.618
54532	C15:0 ANTEISO	21.6	14.711
54532	C15:0 ISO	28.2	14.621
54532	C16:0 iso	3.9	15.626
54532	C16:1 ω11c	2.1	15.757
54532	C17:0 anteiso	0.6	16.722
54532	C17:0 iso	0.7	16.629
54532	C18:1 ω9c	4.6	17.769
54532	C18:2 ω6,9c/C18:0 ANTE	6.5	17.724
54532	Unidentified	0.5	13.927

type of FA analysis: whole cell analysis
method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@ref	country	origin.country	sample type
8930	Turkey	TUR
67770			Turkey meat
124037			Animal, Turkey, cecum

taxonmaps

@ref: 69479
File name: preview.99_51294.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_393;97_1161;98_36831;99_51294&stattab=map
Last taxonomy: Kurthia zopfii subclade
16S sequence: X70321
Sequence Identity:
Total samples: 1957
soil counts: 206
aquatic counts: 206
animal counts: 1454
plant counts: 91

Safety information

risk assessment

@ref	pathogenicity human	biosafety level	biosafety level comment
8930	yes, in single cases	1	Risk group (German classification)
124037		1	Risk group (French classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Kurthia zopfii 16S ribosomal RNA	M58800	1557	ena	1650
20218	Kurthia zopfii DSM:20580 16S ribosomal RNA gene, partial sequence	JN600480	1476	ena	1650
20218	Kurthia zopfii gene for 16S rRNA, partial sequence	AB271740	1479	ena	1650
20218	K.zopfii (NCIMB 9878) 16S rRNA	X70321	1457	ena	1650

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Kurthia zopfii NCTC10597	GCA_900452285	contig	ncbi	1650
66792	Kurthia zopfii NBRC 101529	GCA_007989745	contig	ncbi	1650
66792	Kurthia zopfii strain ATCC 33403	1650.5	wgs	patric	1650
66792	Kurthia zopfii strain DSM 20580	1650.9	wgs	patric	1650
66792	Kurthia zopfii strain NBRC 101529	1650.10	wgs	patric	1650
66792	Kurthia zopfii strain NCTC10597	1650.7	wgs	patric	1650
66792	Kurthia zopfii DSM 20580	2770939571	draft	img	1650
66792	Kurthia zopfii NCTC 10597	2837275893	draft	img	1650
66792	Kurthia zopfii ATCC 33403	2839649258	draft	img	1650
67770	Kurthia zopfii ATCC 33403	GCA_003143955	contig	ncbi	1650
67770	Kurthia zopfii DSM 20580	GCA_004363595	scaffold	ncbi	1650

GC content

@ref	GC-content	method
67770	37.1	thermal denaturation, midpoint method (Tm)
67770	37.6	thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	72	no
motile	yes	84.676	no
gram-positive	yes	92.111	no
anaerobic	no	98.3	yes
aerobic	yes	93.001	yes
halophile	no	72.242	no
spore-forming	yes	85.596	no
thermophile	no	99.153	yes
glucose-util	yes	75.941	no
flagellated	yes	74.823	no
glucose-ferment	no	84.529	no

External links

@ref: 8930

culture collection no.: DSM 20580, ATCC 33403, NCIB 9878, NCTC 10597, CCUG 38890, JCM 6101, CIP 103249, LMG 17318, NBRC 101529, NCIMB 9878, VKM B-1568

straininfo link

@ref: 81167
straininfo: 13979

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	24108326	Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia.	Ruan Z, Wang Y, Song J, Jiang S, Wang H, Li Y, Zhao B, Jiang R, Zhao B	Int J Syst Evol Microbiol	10.1099/ijs.0.056044-0	2013	Bacterial Typing Techniques, Base Composition, Biofuels/microbiology, Bioreactors/microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Phylogeny, Planococcaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry	Genetics
Phylogeny	29299848	Kurthia ruminicola sp. nov., isolated from the rumen contents of a Holstein cow.	Kim MK, Kim ET, Kim SB, Jeong HY, Park BY, Srinivasan S	J Microbiol	10.1007/s12275-018-7285-2	2018	Animals, Bacterial Typing Techniques, Base Composition, Cattle/microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phospholipids/metabolism, Phylogeny, Planococcaceae/classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology	Metabolism
Genetics	30533610	Genome Sequence of Kurthia Type Species Kurthia zopfii Strain ATCC 33403(T).	Goen AE, MacLea KS	Microbiol Resour Announc	10.1128/MRA.00833-18	2018

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
8930	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20580)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-20580
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
41347	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/15026
54532	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 38890)	https://www.ccug.se/strain?id=38890
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
81167	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID13979.1	StrainInfo: A central database for resolving microbial strain identifiers
124037	Curators of the CIP	Collection of Institut Pasteur (CIP 103249)	https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103249

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

oxygen tolerance

murein

fatty acid profile

fatty acids

Isolation, sampling and environmental information

isolation

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference